Hi Harris,

Many thanks for the fast correction, I will test the new version and let
you know.

Best,
Anne


On Sun, Jul 28, 2013 at 6:51 PM, Harris A. Jaffee <hj@jhu.edu> wrote:

> Thank you again for the very precise bug report and your data (off list).
>
> The annotation handlers for the 10000-nearest-transcript chunks were not
> being sent the user's value of 'all', so it defaulted to FALSE.  Having
> fixed that, I found out that these handlers also needed a 'queries' and
> 'Tx' argument, when all=TRUE, which they now have.
>
> The explanation for all this seeming not very well integrated is that the
> 'all' argument was an after thought thrown in by me.  You may be the first
> real user, certainly the first with more than 10000 nearest transcripts.
> I'd be interested in whether it actually helps your analysis.
>
> Sorry about the mc.cores business.  It was irrelevant to the problem.
>
> The fix will appear in bumphunter version 1.1.11, just committed.
>
> On Jul 26, 2013, at 11:14 AM, Harris A. Jaffee wrote:
>
> > Anne,
> >
> > Can you run it with 'verbose=TRUE'?  Also, tell us what your mc.cores
> > value is (This will also appear in the verbose output.)?  If it's >1,
> > please try 'mc.cores=1' to see if that makes any difference.
> >
> > On Jul 26, 2013, at 9:45 AM, Kasper Daniel Hansen wrote:
> >
> >> This sounds weird and it sounds like a bug.  We'll have a look.
> >>
> >> You can (greatly) speed up the process by providing some example
> object(s)
> >> and code to show the error.
> >>
> >> Best,
> >> Kasper
> >>
> >>
> >> On Thu, Jul 25, 2013 at 8:13 PM, Anne Biton <anne.biton@berkeley.edu>
> wrote:
> >>
> >>> Hello,
> >>>
> >>> I am using the function matchGenes of the package bumphunter to
> associate
> >>> many regions of interest with transcripts.
> >>>
> >>> I use all=TRUE in order to get several results per region.
> >>> When I use all=TRUE and a small amount of queries, the output indeed
> >>> contains the columns 'queries' and 'Tx' which give the query index and
> the
> >>> matching transcript.
> >>> But when I use all=TRUE and many regions (when the function starts to
> split
> >>> the data), the output data.frame does not contain anymore these two
> columns
> >>> and it is not possible to know which region is associated with which
> >>> transcript.
> >>> I think there is a problem in the function when the annotation is split
> >>> into chunks of 10000 regions each.
> >>>
> >>> Please let me know if it can be solved!
> >>>
> >>> Best regards,
> >>> Anne
> >>>
> >>>       [[alternative HTML version deleted]]
> >>>
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> >>
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> >>
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